PathBLAST

A network alignment and search tool for comparing protein interaction networks across species to identify protein pathways and complexes that have been conserved by evolution. The basic method searches for high-scoring alignments between pairs of protein interaction paths, for which proteins of the first path are paired with putative orthologs occurring in the same order in the second path. This technique discriminates between true- and false-positive interactions and allows for functional annotation of protein interaction pathways based on similarity to the network of another, well-characterized species.

PathBLAST citations

[…] the well-studied species to the under-studied species). Additionally, network querying can be utilized to predict novel functional modules.Several network querying algorithms have been proposed [–]. PathBLAST [] is one of pioneering network querying algorithms, but it can search only linear pathways and the computational complexity limits the size of the query network. QPath [] can search much lo […]

[…] roblem is a related problem in the context of local alignment [, ]. It matches a small query network to a large target network to find a subnetwork in the target that is similar to the query network. PathBLAST [], TALE [], ABINET [, ] fit in this category. PathBLAST queries a simple path against a target network and returns a ranked list of matching paths and the overlaps among them in the target. […]

library_books

Systems analysis of host–parasite interactions

2015

Wiley Interdiscip Rev Syst Biol Med

PMCID: 4679367

PMID: 26306749

DOI: 10.1002/wsbm.1311

[…] ypothetical proteins was feasible, and alternative biological functions were suggested for some annotated genes. Suthram et al. further analyzed this network using a network alignment approach called PathBLAST, an algorithm that identifies conserved pathways between organisms by identifying conserved proteins and then testing for conserved interactions. Through this, the authors found that few pro […]

library_books

GreedyPlus: An Algorithm for the Alignment of Interface Interaction Networks

2015

Sci Rep

PMCID: 4499810

PMID: 26165520

DOI: 10.1038/srep12074

[…] tein orthology, and then incorporate network information to identify clusters of sequence-similar proteins; these clusters in the network, then, are considered putatively orthologous functional units.PathBLAST, one of the first published PPIN alignment methods, and its successor NetworkBlast, are examples of local network alignment algorithms. Both methods begin by identifying all pairs of protein […]

library_books

The post genomic era of biological network alignment

2015

EURASIP J Bioinform Syst Biol

PMCID: 5270500

PMID: 28194172

DOI: 10.1186/s13637-015-0022-9

[…] We first discuss pairwise and then multiple local network aligners.
PathBLAST [] aligns two PPI networks to identify their conserved pathways. An alignment graph is first built, in which a node represents a pair of putative orthologs (one from each network), and an ed […]

[…] ese PPIs continuously grow in size, they have become increasingly useful for reconstructing PPI networks in an interesting organism.For an interesting organism, several computational methods, such as PathBlast [,] and interologs [,], have been proposed to identify PPIs through the homologs and orthologs. However, most of these methods focus on predicting PPIs in a target organism mapped from one s […]